Protein profile

VK055_1780

tol-pal system protein YbgF

Genome: KpATCC43816

Gene: AIK80393.1 ygbF Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ27
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Amino acids 264
Annotations 5
Features 25
PDB binders 0
Druggability 0.981

Overview

Basic information about this protein and its source genome.

Accession
VK055_1780
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80393.1 ygbF
Status
annotated
Amino acids
264
Structure source
AlphaFold + ColabFold
GO
GO:0070206 The formation of a protein trimer, a macromolecular structure consisting of three noncovalently associated identical or nonidentical subunits. GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. GO:0005515 Binding to a protein. GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall. GO:0043093 A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Periplasmic
ColabFold pLDDT
77.36

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.981
Structure A0A0H3GQ27
Pocket Pocket 2
P2Rank 0.315
Structure A0A0H3GQ27
Pocket Pocket 1
ColabFold model
FPocket 0.748 · Pocket 18
P2Rank 0.03 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 103 / 4744 genomes with a hit
Normalized 0.022

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0070206 The formation of a protein trimer, a macromolecular structure consisting of three noncovalently associated identical or nonidentical subunits.
  • GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
  • GO:0005515 Binding to a protein.
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • GO:0043093 A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
21 26 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
107 128 MobiDBLite mobidb-lite consensus disorder prediction
1 26 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
160 214 Pfam PF13432 Tetratricopeptide repeat
9 20 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
142 263 FunFam G3DSA:1.25.40.10:FF:000109 Cell division coordinator CpoB
1 26 SignalP_EUK SignalP-noTM SignalP-noTM
218 250 Pfam PF13174 Tetratricopeptide repeat
218 250 InterPro IPR019734 Tetratricopeptide repeat
142 254 SUPERFAMILY SSF48452 TPR-like
142 254 InterPro IPR011990 Tetratricopeptide-like helical domain superfamily
6 263 Hamap MF_02066 Cell division coordinator CpoB [cpoB].
6 263 InterPro IPR034706 Cell division coordinator CpoB
145 260 NCBIfam TIGR02795 tol-pal system protein YbgF
145 260 InterPro IPR014162 Cell division coordinator CpoB, C-terminal
35 113 Gene3D G3DSA:1.20.5.110 -
37 105 Pfam PF16331 TolA binding protein trimerisation
37 105 InterPro IPR032519 YbgF, trimerisation domain
253 264 Coils Coil Coil
27 264 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
142 264 Gene3D G3DSA:1.25.40.10 Tetratricopeptide repeat domain
142 264 InterPro IPR011990 Tetratricopeptide-like helical domain superfamily
56 76 Coils Coil Coil
1 8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 26 Phobius SIGNAL_PEPTIDE Signal peptide region

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GQ27
AlphaFold — — full sequence — Viewing
ColabFold VK055_1780
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
2 0.981
11 0.476
8 0.201

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 3.21 0.111
2 1.85 0.036
3 1.78 0.033